Modern Day Palmetto Sharpshooters Battle Flag
The flag that is carried by the Palmetto Sharpshooters, an infantry regiment, at Southern Skirmish Society's re-enactments, is a replica. The damage caused to the modern flag was by accident when a musket was discharge with the muzzle nearly touching the flag, needless to say during the first re-enactment that it was used.
The original Battle Flag carried at the end of the war was a Richmond Depot Issue, Army of Northern Virginia flag which was smuggled away when the Regiment surrender at Appomattox, only fragments remain and these reside in the South Carolina Relic Room.
One other complete flag survives in private hands. This has recently come onto the market and is for sale at Hendershott Museum Consultants at a cost of $195,000. This flag was purchased from the descendants of Lieutenant John P Anderson, of the 27th Michigan. It also comes with Howard Madaus Letter of Authenticity. (I do realize that this information contradicts itself.) This site is worth a look as other flags of the period are depicted, for sale and sold.
Other flags were carried by regiments, and/or flown in their home state, these would be the Bonnie Blue, 1st, 2nd, and 3rd National and State flags.